The principal objective of this study is to elucidate metabolic and biological functions of polyunsaturated fatty acids, docosahexaenoic acid (22:6n3) and arachidonic acid (20:4n6) in the nervous system with particular reference to their modulation by ethanol. The effect of polyunsaturates on the survival of neuronal cells was investigated along with their effect on accumulation of phosphatidylserine (PS), which is thought to be involved in growth factor signaling leading to cell survival. We also found that polyunsaturated fatty acids affected the pineal function since melatonin synthesis was significantly decreased with n-3 deficiency. Polyunsaturated fatty acids, 20:4n6 and 22:6n3, prevented the apoptotic cell death of both Neuro 2A and PC-12 cells, assessed by DNA fragmentation and Hoechst staining. After 4 hours of exposure, only arachidonic acid (up to 25 mM) protected these cells from apoptosis induced by serum deprivation. However, 22:6n3 exerted its protective effect only after enrichment for at least 24 hours. While 22:6n3 was initially incorporated into triglycerides after 4 hours of exposure, a prolonged incubation led to the accumulation of this fatty acid in the aminophospholipids, phosphatidylethanolamine (PE) and PS. Our data suggest that 22:6n3 as a membrane phospholipid constituent, especially in aminophospholipids, may be important for the protective effect. Even the enrichment 18:1n9 did not have any protective effect. The effect of polyunsaturated fatty acids on the accumulation of 22:6n3 in PS and modulation of PS biosynthesis by 22:6n3 was investigated using both animal and cell models, and the phospholipid molecular species were analyzed by electrospray liquid chromatography/mass spectrometry (LC/MS). The induction of n-3 fatty acid deficiency significantly decreased the total polyunsaturated PS without affecting the total amount of polyunsaturated phospholipids in brain microsomes. The decrease in PS was mainly reflected by the incomplete replacement of 18:0:22:6 with 18:0:22:5 species as well as a decline in 18:0:20:4-PS. This reduction of PS was also accompanied by the accumulation of 18:0:22:5-PC, suggesting that the serine base exchange reaction using PC as a substrate may prefer 18:0:22:6-PC in comparison to 18:0:22:5-PC. The serine base exchange activity appeared to be affected by altering 22:6n3 composition in microsomal membranes, since the 18:0:20:4-PS also decreased in the microsomes from n-3 deficient rats without altering the levels of potential substrates in PC and PE. In addition, PS biosynthesis assessed by [3H]serine incorporation decreased significantly after as little as a 30-minute incubation, suggesting that the presence of 22:6n3 species in membrane phospholipids may be important for the serine base exchange reaction, either as substrate molecules or as an enhancer of enzymatic activity. Similarly, C6 glioma cells cultured for 24 hours in docosahexaenoic acid-supplemented media (10-40 mM) significantly increased the synthesis of [3H]PS when compared with unsupplemented or 20:4n6-supplemented cells. Our data show that neuronal and glial PS synthesis is sensitive to changes in the docosahexaenoate levels of phospholipids and suggest that 22:6n3 may be a modulator of PS synthesis. Polyunsaturates, especially 22:6n3, promote the accumulation of PS in contrast to chronic ethanol treatment which was found to significantly decrease the level of polyunsaturated PS without altering total polyunsaturate content in phospholipids.